Diff of the two buildlogs: -- --- b1/build.log 2020-09-10 08:54:58.165131325 +0000 +++ b2/build.log 2020-09-10 08:56:56.396233715 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 9 20:52:45 -12 2020 -I: pbuilder-time-stamp: 1599727965 +I: Current time: Thu Oct 14 05:18:06 +14 2021 +I: pbuilder-time-stamp: 1634138286 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Feb 14 18:47:23 2019 -12 +gpgv: Signature made Fri Feb 15 20:47:23 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -37,136 +37,170 @@ dpkg-source: info: applying fix_tempfile_name_sharing.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/31654/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14677/tmp/hooks/D01_modify_environment starting +debug: Running on codethink-sled15-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/14677/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14677/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='31654' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=14677 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.fTbvcfKFoP/pbuilderrc_UeU4 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.fTbvcfKFoP/b1 --logfile b1/build.log t-coffee_12.00.7fb08c2-4.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.fTbvcfKFoP/pbuilderrc_EQFK --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.fTbvcfKFoP/b2 --logfile b2/build.log t-coffee_12.00.7fb08c2-4.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink-sled10-arm64 4.4.0-189-generic #219-Ubuntu SMP Tue Aug 11 12:24:40 UTC 2020 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.4.0-189-generic #219-Ubuntu SMP Tue Aug 11 12:24:40 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 - -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash - -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat - -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown - -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp - -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash - -rwxr-xr-x 1 root root 97136 Feb 28 2019 date - -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93752 Feb 28 2019 df - -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir - -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 27256 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln - -rwxr-xr-x 1 root root 52544 Jul 26 2018 login - -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 38840 Jan 9 2019 more - -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm - -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 30 20:25 sh -> dash - -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty - -rwsr-xr-x 1 root root 59424 Jan 9 2019 su - -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync - -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar - -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch - -rwxr-xr-x 1 root root 27256 Feb 28 2019 true - -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount - -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/31654/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14264 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 35576 Mar 1 2019 cat + -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown + -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp + -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash + -rwxr-xr-x 1 root root 97136 Mar 1 2019 date + -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93752 Mar 1 2019 df + -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir + -rwxr-xr-x 1 root root 75984 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 31368 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 27256 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34824 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 174304 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 89656 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln + -rwxr-xr-x 1 root root 52544 Jul 27 2018 login + -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 38840 Jan 10 2019 more + -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138736 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35560 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm + -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Oct 14 05:18 sh -> bash + lrwxrwxrwx 1 root root 4 Oct 4 04:48 sh.distrib -> dash + -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty + -rwsr-xr-x 1 root root 59424 Jan 10 2019 su + -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync + -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar + -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch + -rwxr-xr-x 1 root root 27256 Mar 1 2019 true + -rwxr-xr-x 1 root root 14264 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount + -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34824 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/14677/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -235,7 +269,7 @@ Get: 31 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] -Fetched 18.6 MB in 1s (17.8 MB/s) +Fetched 18.6 MB in 1s (18.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19168 files and directories currently installed.) @@ -390,7 +424,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/t-coffee-12.00.7fb08c2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/t-coffee-12.00.7fb08c2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 12.00.7fb08c2-4 dpkg-buildpackage: info: source distribution unstable @@ -430,7 +464,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/evaluate.c:34: + from dp_lib/evaluate_dirichlet.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -482,7 +516,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/evaluate_for_struc.c:34: + from dp_lib/evaluate.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -534,7 +568,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/fsa_dp.c:33: + from dp_lib/evaluate_for_domain.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -586,7 +620,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/evaluate_dirichlet.c:33: + from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -638,7 +672,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/CUSTOM_evaluate_for_struc.c:33: + from dp_lib/fsa_dp.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -690,7 +724,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/evaluate_for_domain.c:33: + from dp_lib/evaluate_for_struc.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -709,28 +743,15 @@ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" -In file included from ./define_header.h:31, - from ./io_lib/io_structures.h:33, - from ./io_lib_header.h:30, - from dev_lib/dev1.c:33: -./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_4_TCOFFEE "x3dna" - ^ ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ -./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" -./programmes_define.h:380: warning: "x3dna" redefined - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" @@ -740,30 +761,43 @@ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" -./programmes_define.h:379: note: this is the location of the previous definition - #define x3dna-ssr_4_TCOFFEE "x3dna" - ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" -./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - ^ ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ -./programmes_define.h:381: warning: "x3dna" redefined - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" -./programmes_define.h:380: note: this is the location of the previous definition - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +In file included from ./define_header.h:31, + from ./io_lib/io_structures.h:33, + from ./io_lib_header.h:30, + from dp_lib/pavie_dp.c:33: +./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_4_TCOFFEE "x3dna" + ^ +./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + ^ +./programmes_define.h:380: warning: "x3dna" redefined + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + +./programmes_define.h:379: note: this is the location of the previous definition + #define x3dna-ssr_4_TCOFFEE "x3dna" + +./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + ^ +./programmes_define.h:381: warning: "x3dna" redefined + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + +./programmes_define.h:380: note: this is the location of the previous definition + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ @@ -791,10 +825,15 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +In file included from ./io_lib_header.h:33, + from dp_lib/evaluate_dirichlet.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/pavie_dp.c:33: + from dev_lib/dev1.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -844,67 +883,82 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, - from dev_lib/dev1.c:33: + from dp_lib/evaluate.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_for_struc.c:34: + from dp_lib/evaluate_for_domain.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ +dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': +dp_lib/evaluate_dirichlet.c:317:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf(fp, "%f\n", &f); + ~~~~~~^~~~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:319:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf(fp, "%f", &f); + ~~~~~~^~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:323:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf(fp, "%f", &f); + ~~~~~~^~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:326:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf(fp, "\n"); + ~~~~~~^~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_for_domain.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ +dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': +dp_lib/evaluate.c:2956:22: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] + fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ +dp_lib/evaluate.c:2956:22: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] +dp_lib/evaluate.c:2956:22: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] +dp_lib/evaluate.c:2956:22: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] In file included from ./io_lib_header.h:33, from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_dirichlet.c:33: + from dp_lib/pavie_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/evaluate.c:34: + from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/pavie_dp.c:33: + from dev_lib/dev1.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ +dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': +dp_lib/evaluate.c:809:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%d ", &res); + ~~~~~~~^~~~~~~~~~~~~~~~~ +dp_lib/evaluate.c:814:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%f %f", &sseq, &mseq); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +dp_lib/evaluate.c:819:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%f %f", &sseq, &mseq); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': dev_lib/dev1.c:89:19: warning: too many arguments for format [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ^~~~~~~~~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': -dp_lib/evaluate_dirichlet.c:317:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf(fp, "%f\n", &f); - ~~~~~~^~~~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:319:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf(fp, "%f", &f); - ~~~~~~^~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:323:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf(fp, "%f", &f); - ~~~~~~^~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:326:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf(fp, "\n"); - ~~~~~~^~~~~~~~~~ +dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': +dp_lib/evaluate.c:7511:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%f %c %*s",&v1, &c1 ); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function 'double** pavie_seq2pavie_aln(Sequence*, char*, char*)': dp_lib/pavie_dp.c:127:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",mat_list[nch++]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC dp_lib/showpair.c dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1079:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system (command); @@ -912,17 +966,12 @@ dp_lib/pavie_dp.c:1081:14: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~^~~~~~~~~ + CC dp_lib/showpair.c dp_lib/pavie_dp.c: In function 'Alignment* pavie_seq2pavie_msa(Sequence*, char*, char*)': dp_lib/pavie_dp.c:1365:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", mat); ~~~~~~~^~~~~~~~~~~~~~~ -dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': -dp_lib/evaluate.c:2956:22: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] - fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ -dp_lib/evaluate.c:2956:22: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] -dp_lib/evaluate.c:2956:22: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] -dp_lib/evaluate.c:2956:22: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] + CC dp_lib/util_domain_dp.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -975,7 +1024,7 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - CC dp_lib/util_domain_dp.c + CC dp_lib/util_domain_dp_drivers.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -1028,31 +1077,73 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': -dp_lib/evaluate.c:809:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%d ", &res); - ~~~~~~~^~~~~~~~~~~~~~~~~ -dp_lib/evaluate.c:814:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%f %f", &sseq, &mseq); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -dp_lib/evaluate.c:819:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%f %f", &sseq, &mseq); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ./define_header.h:31, + from ./io_lib/io_structures.h:33, + from ./io_lib_header.h:30, + from dp_lib/util_domain_dp_drivers.c:33: +./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_4_TCOFFEE "x3dna" + ^ +./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + ^ +./programmes_define.h:380: warning: "x3dna" redefined + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + +./programmes_define.h:379: note: this is the location of the previous definition + #define x3dna-ssr_4_TCOFFEE "x3dna" + +./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + ^ +./programmes_define.h:381: warning: "x3dna" redefined + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + +./programmes_define.h:380: note: this is the location of the previous definition + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + +./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + ^ +./programmes_define.h:382: warning: "x3dna" redefined + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + +./programmes_define.h:381: note: this is the location of the previous definition + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + +./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_mode "saracoffee" + ^ +./programmes_define.h:383: warning: "x3dna" redefined + #define x3dna-ssr_mode "saracoffee" + +./programmes_define.h:382: note: this is the location of the previous definition + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + +./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_update_action "never" + ^ +./programmes_define.h:384: warning: "x3dna" redefined + #define x3dna-ssr_update_action "never" + +./programmes_define.h:383: note: this is the location of the previous definition + #define x3dna-ssr_mode "saracoffee" + +In file included from ./io_lib_header.h:33, + from dp_lib/util_domain_dp.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/showpair.c:32: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ - CC dp_lib/util_domain_dp_drivers.c In file included from ./io_lib_header.h:33, - from dp_lib/util_domain_dp.c:33: + from dp_lib/util_domain_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ -dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': -dp_lib/evaluate.c:7511:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%f %c %*s",&v1, &c1 ); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1078:26: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] sprintf ( command, "cp %s %s", mat_name[a], latest); @@ -1074,10 +1165,11 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC dp_lib/util_dp_cdna_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_domain_dp_drivers.c:33: + from dp_lib/util_dp_cdna_fasta_nw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1127,15 +1219,16 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, - from dp_lib/util_domain_dp_drivers.c:33: + from dp_lib/util_dp_cdna_fasta_nw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ - CC dp_lib/util_dp_cdna_fasta_nw.c + CC dp_lib/util_dp_clean_maln.c + CC dp_lib/util_dp_drivers.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_cdna_fasta_nw.c:33: + from dp_lib/util_dp_clean_maln.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1184,16 +1277,10 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_cdna_fasta_nw.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ - CC dp_lib/util_dp_clean_maln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_clean_maln.c:33: + from dp_lib/util_dp_drivers.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1242,11 +1329,21 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - CC dp_lib/util_dp_drivers.c +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_clean_maln.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_drivers.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ + CC dp_lib/util_dp_est.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_drivers.c:33: + from dp_lib/util_dp_est.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1295,21 +1392,16 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" + CC dp_lib/util_dp_fasta_nw.c In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_clean_maln.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_drivers.c:33: + from dp_lib/util_dp_est.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ - CC dp_lib/util_dp_est.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_est.c:33: + from dp_lib/util_dp_fasta_nw.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1358,12 +1450,6 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_est.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ - CC dp_lib/util_dp_fasta_nw.c dp_lib/util_dp_drivers.c: In function 'char* seq_file2msa_file(char*, char*, char*)': dp_lib/util_dp_drivers.c:1014:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); @@ -1443,10 +1529,11 @@ dp_lib/util_dp_drivers.c:2256:6: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + CC dp_lib/util_dp_fasta_sw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_fasta_nw.c:34: + from dp_lib/util_dp_fasta_sw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1495,64 +1582,11 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - CC dp_lib/util_dp_fasta_sw.c -In file included from ./define_header.h:31, - from ./io_lib/io_structures.h:33, - from ./io_lib_header.h:30, - from dp_lib/util_dp_fasta_sw.c:33: -./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_4_TCOFFEE "x3dna" - ^ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ -./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ^ -./programmes_define.h:380: warning: "x3dna" redefined - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:379: note: this is the location of the previous definition - #define x3dna-ssr_4_TCOFFEE "x3dna" - -./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - ^ -./programmes_define.h:381: warning: "x3dna" redefined - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - -./programmes_define.h:380: note: this is the location of the previous definition - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - ^ -./programmes_define.h:382: warning: "x3dna" redefined - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - -./programmes_define.h:381: note: this is the location of the previous definition - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - -./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_mode "saracoffee" - ^ -./programmes_define.h:383: warning: "x3dna" redefined - #define x3dna-ssr_mode "saracoffee" - -./programmes_define.h:382: note: this is the location of the previous definition - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - -./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_update_action "never" - ^ -./programmes_define.h:384: warning: "x3dna" redefined - #define x3dna-ssr_update_action "never" - -./programmes_define.h:383: note: this is the location of the previous definition - #define x3dna-ssr_mode "saracoffee" - In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_sw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -1611,12 +1645,12 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" + CC dp_lib/util_dp_gotoh_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_generic_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ - CC dp_lib/util_dp_gotoh_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -1670,11 +1704,37 @@ #define x3dna-ssr_mode "saracoffee" CC dp_lib/util_dp_gotoh_sw.c -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_gotoh_nw.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ +dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': +dp_lib/util_dp_drivers.c:382:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); + ^~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dp_lib/util_dp_drivers.c:373:22: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); + ^~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dp_lib/util_dp_drivers.c:386:40: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); + ^~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -1728,6 +1788,11 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_gotoh_nw.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ +In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_sw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol @@ -1736,33 +1801,13 @@ dp_lib/util_dp_gotoh_sw.c:391:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': -dp_lib/util_dp_drivers.c:382:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); - ^~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dp_lib/util_dp_drivers.c:373:22: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); - ^~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dp_lib/util_dp_drivers.c:386:40: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); - ^~~~ +dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': +dp_lib/util_dp_drivers.c:920:22: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] + sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 38 or more bytes (assuming 1037) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); @@ -1825,17 +1870,6 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': -dp_lib/util_dp_drivers.c:920:22: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] - sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 38 or more bytes (assuming 1037) into a destination of size 1000 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_sim.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, @@ -1889,12 +1923,24 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': +dp_lib/util_dp_drivers.c:1854:22: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] + sprintf ( command, "t_coffee -other_pg tc_generic_method.pl -mode=%s -method=%s %s %s%s %s %s%s -tmpdir=%s %s %s", M->executable, M->executable2, M->param1,M->in_flag,infile,M->param2,M->out_flag,outfile,get_tmp_4_tcoffee(),db,M->param); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 71 or more bytes (assuming 6067) into a destination of size 1000 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_ssec_pwaln.c + CC dp_lib/util_dp_suboptimal_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -1947,23 +1993,6 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': -dp_lib/util_dp_drivers.c:1854:22: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] - sprintf ( command, "t_coffee -other_pg tc_generic_method.pl -mode=%s -method=%s %s %s%s %s %s%s -tmpdir=%s %s %s", M->executable, M->executable2, M->param1,M->in_flag,infile,M->param2,M->out_flag,outfile,get_tmp_4_tcoffee(),db,M->param); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 71 or more bytes (assuming 6067) into a destination of size 1000 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC dp_lib/util_dp_suboptimal_nw.c -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_ssec_pwaln.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2017,11 +2046,17 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_suboptimal_nw.c:33: + from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_graph_maln.c +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_suboptimal_nw.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ + CC fastal/diagonal.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2074,13 +2109,6 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -In file included from ./io_lib_header.h:33, - from dp_lib/util_graph_maln.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ - CC fastal/diagonal.c - CC fastal/fastal.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2134,10 +2162,29 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, + from dp_lib/util_graph_maln.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ +In file included from ./io_lib_header.h:33, from fastal/diagonal.c:31: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ +fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': +fastal/diagonal.c:434:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] + system(blast_command); + ~~~~~~^~~~~~~~~~~~~~~ +fastal/diagonal.c:439:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/diagonal.c:440:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/diagonal.c:441:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ + CC fastal/fastal.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2190,25 +2237,13 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': -fastal/diagonal.c:434:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] - system(blast_command); - ~~~~~~^~~~~~~~~~~~~~~ -fastal/diagonal.c:439:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/diagonal.c:440:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/diagonal.c:441:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ + CC fastal/fastal_opt_parsing.c In file included from ./io_lib_header.h:33, from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ - CC fastal/fastal_opt_parsing.c + CC fastal/iteration.c fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:1924:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); @@ -2285,8 +2320,6 @@ fastal/fastal.c:3643:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(aligned_sequence, alignment_length+3, edit_seq_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC fastal/iteration.c - CC fastal/parttree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2339,6 +2372,12 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" + CC fastal/parttree.c +In file included from ./io_lib_header.h:33, + from fastal/iteration.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2392,11 +2431,6 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, - from fastal/iteration.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ -In file included from ./io_lib_header.h:33, from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol @@ -2522,6 +2556,17 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +dp_lib/util_dp_drivers.c: In function 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)': +dp_lib/util_dp_drivers.c:3717:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + sprintf ( dp_mode, "%s", CL->dp_mode); + ^~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from fastal/scoring.c:37: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -2573,7 +2618,6 @@ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/tree.c - CC io_lib/io_func.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2626,6 +2670,13 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +In file included from ./io_lib_header.h:33, + from fastal/tree.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ + CC io_lib/io_func.c + CC io_lib/pb_util_read_seq_util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2678,44 +2729,6 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -In file included from ./io_lib_header.h:33, - from io_lib/io_func.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ -In file included from ./io_lib_header.h:33, - from fastal/tree.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)': -dp_lib/util_dp_drivers.c:3717:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - sprintf ( dp_mode, "%s", CL->dp_mode); - ^~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -io_lib/io_func.c: In function 'int output_raw_score(Alignment*, Alignment*, char*)': -io_lib/io_func.c:1235:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] - if (!A)return NULL; - ^~~~ -io_lib/io_func.c: In function 'int aln2compressed_ps(Alignment*, char*)': -io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -io_lib/io_func.c: In function 'int** read_matrice(char*)': -io_lib/io_func.c:511:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "\n"); - ~~~~~~~^~~~~~~~~~~ -io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': -io_lib/io_func.c:971:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC io_lib/pb_util_read_seq_util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2773,7 +2786,11 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ - CC io_lib/pb_util_read_sequence.c +In file included from ./io_lib_header.h:33, + from io_lib/io_func.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'void getstr(char*, char*)': io_lib/pb_util_read_seq_util.c:269:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(outstr, 100, stdin); @@ -2786,6 +2803,7 @@ io_lib/pb_util_read_seq_util.c:305:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ + CC io_lib/pb_util_read_sequence.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2838,11 +2856,39 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +dp_lib/util_dp_drivers.c: In function 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)': +dp_lib/util_dp_drivers.c:3717:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + sprintf ( dp_mode, "%s", CL->dp_mode); + ^~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +io_lib/io_func.c: In function 'int output_raw_score(Alignment*, Alignment*, char*)': +io_lib/io_func.c:1235:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] + if (!A)return NULL; + ^~~~ +io_lib/io_func.c: In function 'int aln2compressed_ps(Alignment*, char*)': +io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ +io_lib/io_func.c: In function 'int** read_matrice(char*)': +io_lib/io_func.c:511:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "\n"); + ~~~~~~~^~~~~~~~~~~ +io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': +io_lib/io_func.c:971:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_sequence.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ + CC io_lib/tree_util.c io_lib/pb_util_read_sequence.c: In function 'void get_clustal_seq(char*, char*, int*, char*, int)': io_lib/pb_util_read_sequence.c:144:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ @@ -2850,31 +2896,6 @@ io_lib/pb_util_read_sequence.c:149:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] for(i=1;idp_mode); - ^~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC km_coffee/classes.c -km_coffee/Vector.c: In function 'void print_vecs(VectorSet*, char*)': -km_coffee/Vector.c:869:18: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - fprintf(out_F, "%i ", i); - ^~~~~ ~ CC km_coffee/km_coffee.c + CC km_coffee/km_util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -3072,18 +3103,20 @@ km_coffee/km_coffee.c:491:7: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(km_tmp_dir); ~~~~~^~~~~~~~~~~~ - CC km_coffee/km_util.c CC km_coffee/kmeans.c km_coffee/km_util.c: In function 'char* my_make_temp_dir(char*, char*)': km_coffee/km_util.c:96:19: warning: format '%s' expects a matching 'char*' argument [-Wformat=] fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +km_coffee/Vector.c: In function 'void print_vecs(VectorSet*, char*)': +km_coffee/Vector.c:869:18: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + fprintf(out_F, "%i ", i); + ^~~~~ ~ CC t_coffee_lib/t_coffee.c - CC util_lib/aln_compare.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from util_lib/aln_compare.c:34: + from t_coffee_lib/t_coffee.c:35: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -3132,10 +3165,16 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" + CC util_lib/aln_compare.c +In file included from ./io_lib_header.h:33, + from t_coffee_lib/t_coffee.c:35: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from t_coffee_lib/t_coffee.c:35: + from util_lib/aln_compare.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -3184,13 +3223,20 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - CC util_lib/aln_convertion_util.c - CC util_lib/hsearch.c In file included from ./io_lib_header.h:33, from util_lib/aln_compare.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ + CC util_lib/aln_convertion_util.c +t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)': +t_coffee_lib/t_coffee.c:6544:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ +t_coffee_lib/t_coffee.c: In function 'Alignment* t_coffee_dpa(int, char**)': +t_coffee_lib/t_coffee.c:7129:61: warning: too many arguments for format [-Wformat-extra-args] + else { w=seq2dpa_weight (S, "longuest");fprintf ( stderr, "default longuest\n", dpa_weight);} + ^~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -3234,11 +3280,6 @@ ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" -In file included from ./io_lib_header.h:33, - from t_coffee_lib/t_coffee.c:35: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ @@ -3248,6 +3289,24 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +t_coffee_lib/t_coffee.c: In function 'Alignment* km_align_seq_slow(char*, Alignment*, int, char**, int, int)': +t_coffee_lib/t_coffee.c:6783:1: warning: control reaches end of non-void function [-Wreturn-type] + } + ^ +In file included from ./io_lib_header.h:33, + from util_lib/aln_convertion_util.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ +util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': +util_lib/aln_convertion_util.c:4446:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ + CC util_lib/hsearch.c +util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': +util_lib/aln_convertion_util.c:7697:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -3300,38 +3359,23 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)': -t_coffee_lib/t_coffee.c:6544:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -t_coffee_lib/t_coffee.c: In function 'Alignment* t_coffee_dpa(int, char**)': -t_coffee_lib/t_coffee.c:7129:61: warning: too many arguments for format [-Wformat-extra-args] - else { w=seq2dpa_weight (S, "longuest");fprintf ( stderr, "default longuest\n", dpa_weight);} - ^~~~~~~~~~~~~~~~~~~~ -t_coffee_lib/t_coffee.c: In function 'Alignment* km_align_seq_slow(char*, Alignment*, int, char**, int, int)': -t_coffee_lib/t_coffee.c:6783:1: warning: control reaches end of non-void function [-Wreturn-type] - } - ^ +util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': +util_lib/aln_convertion_util.c:7459:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets ( line, VERY_LONG_STRING,fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/aln_convertion_util.c:7478:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/aln_convertion_util.c:7482:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets ( line, VERY_LONG_STRING,fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/hsearch.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/aln_convertion_util.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ CC util_lib/random.c -util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': -util_lib/aln_convertion_util.c:4446:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ CC util_lib/reformat.c -util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': -util_lib/aln_convertion_util.c:7697:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -3384,26 +3428,13 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" + CC util_lib/reformat_struc.c In file included from ./io_lib_header.h:33, from util_lib/reformat.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ -util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': -util_lib/aln_convertion_util.c:7459:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line, VERY_LONG_STRING,fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c:7478:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c:7482:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line, VERY_LONG_STRING,fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC util_lib/reformat_struc.c -util_lib/reformat.c: In function 'int output_suchard_aln(char*, Alignment*)': -util_lib/reformat.c:7441:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ + CC util_lib/util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -3456,6 +3487,95 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +In file included from ./io_lib_header.h:33, + from util_lib/reformat_struc.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ +In file included from ./define_header.h:31, + from ./io_lib/io_structures.h:33, + from ./io_lib_header.h:30, + from util_lib/util.c:52: +./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_4_TCOFFEE "x3dna" + ^ +./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + ^ +./programmes_define.h:380: warning: "x3dna" redefined + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + +./programmes_define.h:379: note: this is the location of the previous definition + #define x3dna-ssr_4_TCOFFEE "x3dna" + +./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + ^ +./programmes_define.h:381: warning: "x3dna" redefined + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + +./programmes_define.h:380: note: this is the location of the previous definition + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + +./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + ^ +./programmes_define.h:382: warning: "x3dna" redefined + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + +./programmes_define.h:381: note: this is the location of the previous definition + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + +./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_mode "saracoffee" + ^ +./programmes_define.h:383: warning: "x3dna" redefined + #define x3dna-ssr_mode "saracoffee" + +./programmes_define.h:382: note: this is the location of the previous definition + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + +./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_update_action "never" + ^ +./programmes_define.h:384: warning: "x3dna" redefined + #define x3dna-ssr_update_action "never" + +./programmes_define.h:383: note: this is the location of the previous definition + #define x3dna-ssr_mode "saracoffee" + +util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': +util_lib/reformat_struc.c:125:18: warning: too many arguments for format [-Wformat-extra-args] + fprintf (out, "ATOM ", lw[1]);//ATOM + ^~~~~~~~ +util_lib/reformat.c: In function 'int output_suchard_aln(char*, Alignment*)': +util_lib/reformat.c:7441:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ +util_lib/reformat_struc.c: In function 'Ca_trace* simple_read_ca_trace(char*)': +util_lib/reformat_struc.c:370:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%*s" ); + ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:372:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%*s" ); + ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:378:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat_struc.c:405:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%*s" ); + ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:407:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%*s" ); + ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:416:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ./io_lib_header.h:33, + from util_lib/util.c:52: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ util_lib/reformat.c: In function 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)': util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) @@ -3586,6 +3706,10 @@ util_lib/reformat.c:12390:31: note: in expansion of macro 'ATOI_ACTION' D1->A=shuffle_aln (D1->A, ATOI_ACTION(1), ACTION(2), ACTION (3)); ^~~~~~~~~~~ +util_lib/util.c: In function 'int cherry(int, char**)': +util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ util_lib/reformat.c:12901:36: warning: null argument where non-null required (argument 1) [-Wnonnull] else if (strstr (ACTION(1), "h")) ^ @@ -3685,11 +3809,6 @@ util_lib/reformat.c:13620:8: note: in expansion of macro 'ATOI_ACTION' p3=ATOI_ACTION(5); ^~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/reformat_struc.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ util_lib/reformat.c: In function 'int output_header_mat(int**, char*)': util_lib/reformat.c:14324:1: warning: no return statement in function returning non-void [-Wreturn-type] } @@ -3800,6 +3919,10 @@ util_lib/reformat.c:4602:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%s",name); ~~~~~~~^~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int dump_nfc(char*, char*)': +util_lib/util.c:4455:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ util_lib/reformat.c: In function 'int fscanf_seq_name(FILE*, char*)': util_lib/reformat.c:5636:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", name); @@ -3823,29 +3946,15 @@ util_lib/reformat.c:6423:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %d", name,&i); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': -util_lib/reformat_struc.c:125:18: warning: too many arguments for format [-Wformat-extra-args] - fprintf (out, "ATOM ", lw[1]);//ATOM - ^~~~~~~~ -util_lib/reformat_struc.c: In function 'Ca_trace* simple_read_ca_trace(char*)': -util_lib/reformat_struc.c:370:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%*s" ); - ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:372:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%*s" ); - ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:378:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat_struc.c:405:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%*s" ); - ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:407:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%*s" ); - ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:416:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int set_nproc(int)': +util_lib/util.c:5488:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ +util_lib/util.c: In function 'char* vremove3(char*, char*)': +util_lib/util.c:6920:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ + CC util_lib/util_aln_analyze.c util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': util_lib/reformat.c:14165:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); @@ -3873,81 +3982,6 @@ util_lib/reformat.c:14396:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC util_lib/util.c -In file included from ./define_header.h:31, - from ./io_lib/io_structures.h:33, - from ./io_lib_header.h:30, - from util_lib/util.c:52: -./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_4_TCOFFEE "x3dna" - ^ -./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ^ -./programmes_define.h:380: warning: "x3dna" redefined - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:379: note: this is the location of the previous definition - #define x3dna-ssr_4_TCOFFEE "x3dna" - -./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - ^ -./programmes_define.h:381: warning: "x3dna" redefined - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - -./programmes_define.h:380: note: this is the location of the previous definition - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - ^ -./programmes_define.h:382: warning: "x3dna" redefined - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - -./programmes_define.h:381: note: this is the location of the previous definition - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - -./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_mode "saracoffee" - ^ -./programmes_define.h:383: warning: "x3dna" redefined - #define x3dna-ssr_mode "saracoffee" - -./programmes_define.h:382: note: this is the location of the previous definition - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - -./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_update_action "never" - ^ -./programmes_define.h:384: warning: "x3dna" redefined - #define x3dna-ssr_update_action "never" - -./programmes_define.h:383: note: this is the location of the previous definition - #define x3dna-ssr_mode "saracoffee" - -In file included from ./io_lib_header.h:33, - from util_lib/util.c:52: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ -util_lib/util.c: In function 'int cherry(int, char**)': -util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -util_lib/util.c: In function 'int dump_nfc(char*, char*)': -util_lib/util.c:4455:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -util_lib/util.c: In function 'int set_nproc(int)': -util_lib/util.c:5488:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -util_lib/util.c: In function 'char* vremove3(char*, char*)': -util_lib/util.c:6920:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ - CC util_lib/util_aln_analyze.c util_lib/util.c: In function 'FILE* hsort_file(FILE*, int, int, size_t, int, int, int (*)(const void*, const void*, int, int, size_t), void* (*)(void*, void*, size_t))': util_lib/util.c:281:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[--l]*/ @@ -3989,17 +4023,6 @@ util_lib/util.c:1813:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "\n"); ~~~~~~~^~~~~~~~~~ -t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': -t_coffee_lib/t_coffee.c:5621:32: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] - sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); - ^~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:873, - from t_coffee_lib/t_coffee.c:27: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) into a destination of size 1000 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int perl_strstr(char*, char*)': util_lib/util.c:2468:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d", &r); @@ -4076,7 +4099,6 @@ util_lib/util.c:7554:2: warning: second parameter of 'va_start' not last named argument [-Wvarargs] va_start (ap, usage); ^~~~~~~~ - CC util_lib/util_analyse_constraints_list.c util_lib/util.c: In function 'char** get_parameter(char*, int*, char*)': util_lib/util.c:7821:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); @@ -4104,6 +4126,31 @@ util_lib/util.c:10370:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ +In file included from ./io_lib_header.h:33, + from util_lib/util_aln_analyze.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ +util_lib/util_aln_analyze.c: In function 'Alignment* sar_analyze(Alignment*, Alignment*, char*)': +util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ +util_lib/util_aln_analyze.c: In function 'Alignment* or_scan(Alignment*, Alignment*, char*)': +util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ + CC util_lib/util_analyse_constraints_list.c +t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': +t_coffee_lib/t_coffee.c:5621:32: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] + sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); + ^~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:873, + from t_coffee_lib/t_coffee.c:27: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) into a destination of size 1000 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -4157,23 +4204,10 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, - from util_lib/util_aln_analyze.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ -util_lib/util_aln_analyze.c: In function 'Alignment* sar_analyze(Alignment*, Alignment*, char*)': -util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -In file included from ./io_lib_header.h:33, from util_lib/util_analyse_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ -util_lib/util_aln_analyze.c: In function 'Alignment* or_scan(Alignment*, Alignment*, char*)': -util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ CC util_lib/util_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, @@ -4244,42 +4278,6 @@ util_lib/util_constraints_list.c:2852:19: warning: too many arguments for format [-Wformat-extra-args] x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); ^~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': -util_lib/util_constraints_list.c:582:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] - chdir (tdir); - ~~~~~~^~~~~~ -util_lib/util_constraints_list.c:585:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] - chdir (cdir); - ~~~~~~^~~~~~ -util_lib/util_constraints_list.c: In function 'char* method_file_tag2value(char*, char*)': -util_lib/util_constraints_list.c:1151:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line,LONG_STRING, fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'TC_method* method_file2TC_method(char*)': -util_lib/util_constraints_list.c:1194:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line,LONG_STRING, fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'int read_cpu_in_list(char*)': -util_lib/util_constraints_list.c:2600:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - if ( c=='C')fscanf( fp, "PU %d\n", &cpu); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'int read_seq_in_list(char*, int*, char***, char***, Genomic_info**)': -util_lib/util_constraints_list.c:2918:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%d\n", &max_nseq); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c:2923:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%*s %d %*s\n", &l); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c:2955:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c:2980:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets (line , 200 , fp); - ~~~~~~^~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)': -util_lib/util_constraints_list.c:4054:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_declare.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, @@ -4333,6 +4331,42 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': +util_lib/util_constraints_list.c:582:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] + chdir (tdir); + ~~~~~~^~~~~~ +util_lib/util_constraints_list.c:585:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] + chdir (cdir); + ~~~~~~^~~~~~ +util_lib/util_constraints_list.c: In function 'char* method_file_tag2value(char*, char*)': +util_lib/util_constraints_list.c:1151:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets ( line,LONG_STRING, fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'TC_method* method_file2TC_method(char*)': +util_lib/util_constraints_list.c:1194:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets ( line,LONG_STRING, fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'int read_cpu_in_list(char*)': +util_lib/util_constraints_list.c:2600:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + if ( c=='C')fscanf( fp, "PU %d\n", &cpu); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'int read_seq_in_list(char*, int*, char***, char***, Genomic_info**)': +util_lib/util_constraints_list.c:2918:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%d\n", &max_nseq); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c:2923:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%*s %d %*s\n", &l); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c:2955:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c:2980:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets (line , 200 , fp); + ~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)': +util_lib/util_constraints_list.c:4054:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_declare.c:37: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -4519,11 +4553,6 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -In file included from ./io_lib_header.h:33, - from util_lib/util_job_handling.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -4577,6 +4606,11 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, + from util_lib/util_job_handling.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ +In file included from ./io_lib_header.h:33, from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol @@ -4870,12 +4904,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/14677/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14677/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/31654 and its subdirectories -I: Current time: Wed Sep 9 20:54:56 -12 2020 -I: pbuilder-time-stamp: 1599728096 +I: removing directory /srv/workspace/pbuilder/14677 and its subdirectories +I: Current time: Thu Oct 14 05:19:54 +14 2021 +I: pbuilder-time-stamp: 1634138394